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(-) Description

Title :  CRYSTAL STRUCTURE OF TRNA G26 METHYLTRANSFERASE TRM1 IN APO FORM FROM PYROCOCCUS HORIKOSHII
 
Authors :  Ihsanawati, M. Shirouzu, Y. Bessho, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  24 Jul 06  (Deposition) - 24 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Trna Modification Enzyme, Guanine 26, N(2), N(2)-Dimethyltransferase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Ihsanawati, M. Nishimoto, K. Higashijima, M. Shirouzu, H. Grosjean, Y. Bessho, S. Yokoyama
Crystal Structure Of Trna N(2), N(2)-Guanosine Dimethyltransferase Trm1 From Pyrococcus Horikoshii
J. Mol. Biol. V. 383 871 2008
PubMed-ID: 18789948  |  Reference-DOI: 10.1016/J.JMB.2008.08.068

(-) Compounds

Molecule 1 - N(2),N(2)-DIMETHYLGUANOSINE TRNA METHYLTRANSFERASE
    Chains: A
    EC Number: 2.1.1.32
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: BL21-CODONPLUS (DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 1-378
    Gene: TRM1
    Mutation: YES
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953
    Synonym: TRNA(GUANINE-26,N(2)-N(2)) METHYLTRANSFERASE, TRNA 2,2- DIMETHYLGUANOSINE-26 METHYLTRANSFERASE, TRNA(M(2,2)G26) DIMETHYLTRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:220 , LEU A:281 , LYS A:282 , GLU A:315 , LEU A:316 , ASP A:317 , HIS A:356 , PHE A:357 , HOH A:433BINDING SITE FOR RESIDUE GOL A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DUL)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:274 -Pro A:275

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DUL)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_TRM1PS51626 Trm1 methyltransferase domain profile.TRM1_PYRHO7-378  1A:4-375
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_TRM1PS51626 Trm1 methyltransferase domain profile.TRM1_PYRHO7-378  1A:4-375
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SAM_MT_TRM1PS51626 Trm1 methyltransferase domain profile.TRM1_PYRHO7-378  2A:4-375

(-) Exons   (0, 0)

(no "Exon" information available for 2DUL)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:367
 aligned with TRM1_PYRHO | O59493 from UniProtKB/Swiss-Prot  Length:381

    Alignment length:375
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375     
           TRM1_PYRHO     6 LIEVQEGKAKILIPKAESIYDSPVFYNPRMALNRDIVVVLLNILNPKIVLDALSATGIRGIRFALETPAEEVWLNDISEDAYELMKRNVMLNFDGELRESKGRAILKGEKTIVINHDDANRLMAERHRYFHFIDLDPFGSPMEFLDTALRSAKRRGILGVTATDGAPLCGAHPRACLRKYLAVPLRGELCHEVGTRILVGVIARYAAKYDLGIDVILAYYKDHYFRAFVKLKDGARKGDETLEKLGYIYFDDKTGKFELEQGFLPTRPNAYGPVWLGPLKDEKIVSKMVKEAESLSLARKKQALKLLKMIDQELDIPLFYDTHAIGRRLKIETKKVEEIISALREQGYEATRTHFSPTGIKTSAPYEVFIETIKR 380
               SCOP domains d2dula1 A:3-37        7 N(2),N(2)-dimethylguanosine tRNA methyltransferase Trm1                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeee.--------....hhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhh....ee...eeeee...eeeeee.hhhhhhhhh...eeeeee.....hhhhhhhhhhheeeeeeeeeee.hhhhhh..hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeeehhhhhhhhhh.eeeeee......eeeee.........eeeee.....hhhhhhhhhhhhhh....hhhhhhhhhhhhhhh......eehhhhhhhhh....hhhhhhhhhhhh...eeee..eeeeeee..hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -SAM_MT_TRM1  PDB: A:4-375 UniProt: 7-378                                                                                                                                                                                                                                                                                                                                            -- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dul A   3 LIEVQEGKAKILIP--------PVFYNPRMALNRDIVVVLLNILNPKIVLDALSATGIRGIRFALETPAEEVWLNDISEDAYELMKRNVMLNFDGELRESKGRAILKGEKTIVINHDDANRLMAERHRYFHFIDLDPFGSPMEFLDTALRSAKRRGILGVTATDGAPLCGAHPRACLRKYLAVPLRGELCHEVGTRILVGVIARYAAKYDLGIDVILAYYKDHYFRAFVKLKDGARKGDETLEKLGYIYFDDKTGKFELEQGFLPTRPNAYGPVWLGPLKDEKIVSKMVKEAESLSLARKKQALKLLKMIDQELDIPLFYDTHAIGRRLKIETKKVEEIISALREQGYEATRTHFSPTGIKTSAPYEVFIETIKR 377
                                    12   |     -  |     32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372     
                                        16       25
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DUL)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DUL)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (TRM1_PYRHO | O59493)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0004809    tRNA (guanine-N2-)-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + tRNA containing guanine = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine.
    GO:0000049    tRNA binding    Interacting selectively and non-covalently with transfer RNA.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0030488    tRNA methylation    The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
    GO:0008033    tRNA processing    The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.

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 Related Entries

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        TRM1_PYRHO | O59493: 2ejt 2eju 2ytz

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